Covid-19 Omicron outbreak: South Africa's cases are beginning to soar again

A health worker administers a Covid-19 vaccine to a student during a rural vaccination drive in Mpumalanga, South Africa. Photo / Getty Images

South Africa's Covid cases are beginning to soar again because of two new mutated sub-variants of Omicron that could be dodging the body's immunity, according to scientists.

In the last two weeks, South Africa's daily new cases have gone up six-fold to almost 10,000 a day, with one in every four tests coming back positive. This means the country is now staring down the barrel of a fifth wave.

Scientists scrambling to find out what's causing the uptick in cases say it could be linked to two new offshoots of the original omicron variant (BA.1) which hit South Africa in December, called BA.4 and BA.5.

Both sub-variants have a mutation on the spike protein. This means the virus might be able to evade immunity acquired from past infections or a vaccine, according to Dr Nicole Wolter of South Africa's National Institute for Communicable Diseases.

On Wednesday, Tedros Ghebreyesus, head of the World Health Organisation, confirmed that the two sub-variants were behind the surge. But emphasised that it was "too soon to know whether these new sub-variants can cause more severe disease than other Omicron sub-variants".

Widespread apathy

Official statistics say that South Africa is by far the worst-hit country on the continent. There have been more than 300,000 excess deaths - the number of deaths above the yearly average - since the pandemic began, according to the South African Medical Research Council.

The potential fifth wave comes at a time when Africa's most industrialised nation has almost completely lost interest in Covid-19. While both the Beta and Delta variant waves were utterly devastating for South Africa, the latest Omicron wave in December was relatively mild.

The lack of severity in December has contributed to widespread apathy about the disease. Local reports say that vaccination rates are down to an all-time low, even though more than 50 per cent of South Africans have not been vaccinated.

Health workers prepare doses of the Covid-19 vaccine during a rural vaccination drive by Broadreach NGO. Photo / Getty Images

Last week, just over 45,000 people got vaccinated in the country, compared with more than a million in late August 2021.

Estimates suggest that South Africa has an extraordinarily high level of natural immunity, with so-called seropositivity rates hovering at around 90 per cent. However, it's not all good news. The hard-won natural immunity will slowly be waning and one recent study indicates that this natural protection may not stop people from getting reinfected.

A team of scientists including Professor Alex Sigal, the scientist at the University of KwaZulu-Natal who originally found the Beta variant, shows that unvaccinated people who have previously had BA.1 (Omicron) have little protection against infection with BA.4 or BA.5.

While the research has not been peer-reviewed yet, it did offer a strong dose of hope. Prof Sigal's team found that those who had been vaccinated and previously had BA.1 were much better protected.

Scientists say the new sub-variants offer us clues as to how the pandemic will develop, not just into a myriad of different variants but into a vast sub-variant family tree."What we are seeing now, or at least maybe the first signs, is not completely new variants emerging, but current variants are starting to create lineages of themselves," Dr Tulio de Oliveira, director of South Africa's KwaZulu-Natal Research and Innovation Sequencing Platform, told the New York Times earlier this week.

What happens in South Africa, which has an average age of 28, does not translate easily to China with its average age of 38 and a wholly different social structure.

However, some scientists say that the fact that BA.2 - another omicron sub-variant that is genetically similar to BA.4 and BA.5 - has already spread around Europe might blunt the new mutation's effectiveness in countries like the UK, France and Italy.

Moreover, the fact that summer is coming up in the northern hemisphere might help limit infections because more social interactions will be held outside.